Outcomes and prognostic factors among patients with brain metastases (BM) have been widely studied, but seldom for the non-elderly. Heart rate variability (HRV) is a physiological phenomenon and has been shown as a survival prognostic factor in cancer patients. This study aimed to evaluate the outcomes and prognosis among non-elderly BM patients with the incorporation of HRV analysis. Forty non-elderly BM patients treated using whole brain radiotherapy (WBRT) were studied from January 2010 prospectively with 5-min electrocardiography (ECG) recordings. Individualized HRV was generated by the ECG, and the time domain HRV index SDNN was chosen for survival analysis. The median overall survival (OS) for the entire group was 6.21 months. Univariate analysis revealed that a KPS < 80 (p = 0.019) and an SDNN < 10 ms (p = 0.007) demonstrated statistical significance for OS; multivariate analysis confirmed that a KPS < 80 (p = 0.004; HR = 3.060, CI = 1.437-6.517) and an SDNN < 10 ms (p = 0.010; HR = 2.664, CI = 1.262-5.624) were independent prognostic factors. Prospective studies for risk stratification among non-elderly BM patients based on our results are warranted to validate our findings.